No one was injured in the mishap that took place at 5:53 AM.
Services were disrupted on the Central Line of Mumbai suburban railway, while they were suspended on the Kalyan-Karjat line, they said.
Restoration work is underway.
The incident comes a day after the Ajmer-Sealdah express derailed while it was crossing a bridge near Rura Railway Station in Kanpur Rural district of Uttar Pradesh, leaving 2 people dead and 62 passengers injured.